Hi Bruce, Below is the output: ############################USER=k0933235 LOGNAME=k0933235 HOME=/home/k0933235 PATH=/software/system/fsl/fsl-4.1.5//bin:/software/system/fsl/fsl-4.1.5//etc/fslconf/fsl.csh:/software/system/freesurfer/freesurfer-4.5.0//bin:/software/system/freesurfer/freesurfer-4.5.0//fsfast/bin:/software/system/fsl/fsl-4.1.8/bin:/software/system/freesurfer/freesurfer-4.5.0//mni/bin:/cns_zfs/cns_sge/bin/linux-x64:/software/local/bin:/software/system/bin:/software/system/matlab/matlab-7.8.0/bin:/software/system/fsl/fsl-4.1.8/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/software/system/mri3dX/mri3dX_v563:/software/system/surfrelax/TFI/bin:/software/system/ITK/ITK-2.0/bin:/software/local/camino/camino/bin:/software/system/minc-toolkit/20121004/bin MAIL=/var/spool/mail/k0933235 SHELL=/bin/tcsh SSH_CLIENT=137.73.249.51 51517 22 SSH_CONNECTION=137.73.249.51 51517 194.83.137.60 22 SSH_TTY=/dev/pts/21 TERM=xterm DISPLAY=localhost:28.0 SELINUX_ROLE_REQUESTED= SELINUX_LEVEL_REQUESTED= SELINUX_USE_CURRENT_RANGE= HOSTTYPE=x86_64-linux VENDOR=unknown OSTYPE=linux MACHTYPE=x86_64 SHLVL=1 PWD=/home/k0933235 GROUP=k093 HOST=cnslnx1.iop.kcl.ac.uk REMOTEHOST=pc249-51.firepass.kcl.ac.uk HOSTNAME=cnslnx1.iop.kcl.ac.uk G_BROKEN_FILENAMES=1 LANG=en_US.UTF-8 LESSOPEN=|/usr/bin/lesspipe.sh %s QTDIR=/usr/lib64/qt-3.3 QTINC=/usr/lib64/qt-3.3/include QTLIB=/usr/lib64/qt-3.3/lib PAGER=less EDITOR=vim FSLDIR=/software/system/fsl/fsl-4.1.5/ FSLOUTPUTTYPE=NIFTI_GZ FSLMULTIFILEQUIT=TRUE FSLTCLSH=/software/system/fsl/fsl-4.1.8/bin/fsltclsh FSLWISH=/software/system/fsl/fsl-4.1.8/bin/fslwish FSLLOCKDIR= FSLMACHINELIST= FSLREMOTECALL= FSLQUEUE=rhe5b FSLCONFDIR=/software/system/fsl/fsl-4.1.8/config FSLMACHTYPE=linux_64-gcc4.4 LD_LIBRARY_PATH=/cns_zfs/cns_sge/lib/linux-x64:/software/system/qwt/qwt-4.2.0/lib:/software/system/VTK/VTK-5.0.1/lib SGE_ROOT=/cns_zfs/cns_sge SGE_CELL=default SGE_CLUSTER_NAME=p3370 SGE_QMASTER_PORT=3369 SGE_EXECD_PORT=3370 MANPATH=/usr/share/man BRAINTOOLSDIR=/software/system/mri3dX/mri3dX_v563 BrainLibFont=-adobe-helvetica-medium-r-*-*-*-120-*-*-*-*-*-* TFIDIR=/software/system/surfrelax/TFI LIBGL_ALWAYS_INDIRECT=y FREESURFER_HOME=/software/system/freesurfer/freesurfer-4.5.0/ SUBJECTS_DIR=/home/k0933235/paul/PREDEP_Structural/subjects3 FUNCTIONALS_DIR=/software/system/freesurfer/freesurfer-4.5.0//sessions OS=Linux FS_OVERRIDE=0 FSFAST_HOME=/software/system/freesurfer/freesurfer-4.5.0//fsfast MINC_BIN_DIR=/software/system/freesurfer/freesurfer-4.5.0//mni/bin MNI_DIR=/software/system/freesurfer/freesurfer-4.5.0//mni MINC_LIB_DIR=/software/system/freesurfer/freesurfer-4.5.0//mni/lib MNI_DATAPATH=/software/system/freesurfer/freesurfer-4.5.0//mni/data FSL_DIR=/software/system/fsl/fsl-4.1.8 LOCAL_DIR=/software/system/freesurfer/freesurfer-4.5.0//local FSF_OUTPUT_FORMAT=nii FMRI_ANALYSIS_DIR=/software/system/freesurfer/freesurfer-4.5.0//fsfast MNI_PERL5LIB=/software/system/freesurfer/freesurfer-4.5.0//mni/lib/perl5/5.8.5 PERL5LIB=/software/system/freesurfer/freesurfer-4.5.0//mni/lib/perl5/5.8.5 FSL_BIN=/software/system/fsl/fsl-4.1.8/bin FSLDISPLAY=/usr/bin/display FSLCONVERT=/usr/bin/convert FIX_VERTEX_AREA= ############################# Thanks Paul> Date: Tue, 19 Feb 2013 17:50:05 -0500
From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] mri_ca_label problem
just to rule out a longshot, can you send me the output of printenv?
On Tue, 19 Feb 2013, paul horton wrote:
Hi Bruce,
When I run recon -all the last thing it prints before going to the command prompt is
'recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013'
and when I run the stand alone command, i.e. mri_ca_label, the last thing it prints before going to the command prompt is
'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt'
I hope this information helps.
Thanks
Paul
Date: Tue, 19 Feb 2013 17:28:52 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_ca_label problem
and that's the last thing it prints before returning to a prompt? On Tue, 19 Feb 2013, paul horton wrote:
Hi Bruce,
Yes this is within recon-all. I have also tried it as a stand alone
command
but it stops at the same place, i.e. when the function outputs the
following
statement: 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt'. The file
'aseg.auto_noCCseg.mgz'
is not saved but the file 'aseg.auto_noCCseg.label_intensities.txt' is. Yes, it is writeable and there is enough disk space. The only error messages I get refer to the functions not finding the relevant files as they were not saved. I have attached the log below:
#--------------------------------------
#@# SubCort Seg Mon Feb 18 19:02:14 GMT 2013
mri_ca_label -align -nobigventricles norm.mgztransforms/talairach.m3z/software/system/freesurfer/freesurfer-4.5.0//avera
ge/RB_all_2008-03-26.gca
aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes...
reading classifier arrayfrom/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26
.gca
...
reading input volume from norm.mgz...
average std[0] = 6.9
reading transform from transforms/talairach.m3z...
zcat transforms/talairach.m3z
Atlas used for the 3D morphwas/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.
gca
average std = 6.9 using min determinant for regularization = 4.7
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15151 (27)
mri peak = 0.15062 (23)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, overlap=0.484)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, peak
=
22), gca=22.3
gca peak = 0.14982 (20)
mri peak = 0.16025 (24)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, overlap=0.766)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels,
peak =
20), gca=20.5
gca peak = 0.28003 (97)
mri peak = 0.11295 (106)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels,
overlap=0.353)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = 104), gca=104.3
gca peak = 0.18160 (96)
mri peak = 0.12433 (104)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels,
overlap=0.638)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = 101), gca=100.8
gca peak = 0.27536 (62)
mri peak = 0.08252 (69)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, overlap=0.818)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak =
68),
gca=68.2
gca peak = 0.32745 (63)
mri peak = 0.07934 (66)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, overlap=1.000)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak =
65),
gca=64.6
gca peak = 0.08597 (105)
mri peak = 0.06861 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
voxels,
overlap=0.744)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
voxels,
peak = 108), gca=107.6
gca peak = 0.09209 (106)
mri peak = 0.07113 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, overlap=0.820)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, peak = 106), gca=106.0
gca peak = 0.07826 (63)
mri peak = 0.02785 (72)
Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, overlap=0.547)
Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, peak
=
71), gca=70.9
gca peak = 0.08598 (64)
mri peak = 0.02894 (68)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, overlap=0.642)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
peak =
69), gca=68.8
gca peak = 0.24164 (71)
mri peak = 0.13663 (85)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels,
overlap=0.000)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = 82), gca=81.7
gca peak = 0.18227 (75)
mri peak = 0.14739 (80)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels,
overlap=0.988)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = 77), gca=76.9
gca peak = 0.10629 (62)
mri peak = 0.05203 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.948)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
peak =
64), gca=63.5
gca peak = 0.11668 (59)
mri peak = 0.05041 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, overlap=0.926)
Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels,
peak
= 63), gca=63.4
gca peak = 0.17849 (88)
mri peak = 0.09573 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
voxels,
overlap=0.601)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
voxels,
peak = 95), gca=94.6
gca peak = 0.16819 (86)
mri peak = 0.10076 (95)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
voxels,
overlap=0.590)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
voxels,
peak = 92), gca=92.5
gca peak = 0.41688 (64)
mri peak = 0.07820 (67)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels,
overlap=1.000)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = 66), gca=65.6
gca peak = 0.42394 (62)
mri peak = 0.10919 (71)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels,
overlap=0.434)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = 70), gca=69.8
gca peak = 0.10041 (96)
mri peak = 0.07146 (97)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, overlap=0.910)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, peak
=
98), gca=98.4
gca peak = 0.13978 (88)
mri peak = 0.06159 (103)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, overlap=0.376)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, peak
=
99), gca=99.0
gca peak = 0.08514 (81)
mri peak = 0.06222 (85)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
overlap=0.964)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), gca=81.0
gca peak = 0.09624 (82)
mri peak = 0.09383 (84)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels,
overlap=0.815)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = 84), gca=84.0
gca peak = 0.07543 (88)
mri peak = 0.05306 (86)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, overlap=0.765)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = 92), gca=92.4
gca peak = 0.12757 (95)
mri peak = 0.05862 (107)
Right_VentralDC: unreasonable value (111.6/107.0), not in range [80,
110] -
rejecting
gca peak = 0.17004 (92)
mri peak = 0.06574 (111)
Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110]
rejecting
gca peak = 0.21361 (36)
mri peak = 0.12619 (24)
Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels,
overlap=0.000)
Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = 25), gca=25.2
gca peak = 0.26069 (23)
mri peak = 0.16285 (24)
Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels,
overlap=0.640)
Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak =
21),
gca=20.7
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak CSF = 0.14367 (38)
gca peak Left_Accumbens_area = 0.57033 (70)
gca peak Left_VentralDC = 0.17004 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.65201 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.31129 (32)
gca peak Right_Accumbens_area = 0.30219 (72)
gca peak Right_VentralDC = 0.12757 (95)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.72939 (42)
gca peak WM_hypointensities = 0.14821 (82)
gca peak non_WM_hypointensities = 0.10354 (53)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.08 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 0.86 x + 0.0
Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 (was 100.8)
Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5
(was
104.3)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.14515 (23)
mri peak = 0.15062 (23)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, overlap=0.897)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, peak
=
24), gca=23.6
gca peak = 0.19392 (21)
mri peak = 0.16025 (24)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, overlap=0.745)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels,
peak =
21), gca=21.0
gca peak = 0.25607 (102)
mri peak = 0.11295 (106)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels,
overlap=1.000)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105), gca=104.5
gca peak = 0.17462 (103)
mri peak = 0.12433 (104)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels,
overlap=0.999)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = 103), gca=103.0
gca peak = 0.24759 (68)
mri peak = 0.08252 (69)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, overlap=0.999)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak =
68),
gca=68.0
gca peak = 0.28061 (65)
mri peak = 0.07934 (66)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, overlap=0.999)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak =
62),
gca=61.8
gca peak = 0.08360 (108)
mri peak = 0.06861 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
voxels,
overlap=0.831)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
voxels,
peak = 108), gca=108.0
gca peak = 0.09206 (106)
mri peak = 0.07113 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, overlap=0.820)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, peak = 106), gca=106.0
gca peak = 0.06916 (71)
mri peak = 0.02785 (72)
Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, overlap=0.733)
Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, peak
=
69), gca=69.2
gca peak = 0.08227 (69)
mri peak = 0.02894 (68)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, overlap=0.734)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
peak =
69), gca=69.0
gca peak = 0.22329 (81)
mri peak = 0.13663 (85)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels,
overlap=1.000)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 81), gca=81.0
gca peak = 0.18180 (77)
mri peak = 0.14739 (80)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels,
overlap=0.937)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = 77), gca=77.0
gca peak = 0.10419 (63)
mri peak = 0.05203 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.982)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
peak =
65), gca=64.6
gca peak = 0.12084 (64)
mri peak = 0.05041 (65)
Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, overlap=0.985)
Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels,
peak
= 62), gca=62.4
gca peak = 0.17137 (94)
mri peak = 0.09573 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
voxels,
overlap=0.978)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
voxels,
peak = 94), gca=94.0
gca peak = 0.15715 (93)
mri peak = 0.10076 (95)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
voxels,
overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
voxels,
peak = 93), gca=93.0
gca peak = 0.32238 (65)
mri peak = 0.07820 (67)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels,
overlap=1.000)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = 65), gca=65.0
gca peak = 0.49832 (70)
mri peak = 0.10919 (71)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels,
overlap=1.000)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = 70), gca=70.0
gca peak = 0.10606 (98)
mri peak = 0.07146 (97)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, overlap=0.901)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, peak
=
98), gca=98.0
gca peak = 0.12505 (99)
mri peak = 0.06159 (103)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, overlap=0.961)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, peak
=
99), gca=99.0
gca peak = 0.08514 (81)
mri peak = 0.06222 (85)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
overlap=0.964)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), gca=81.0
gca peak = 0.09838 (78)
mri peak = 0.09383 (84)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels,
overlap=0.982)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = 78), gca=78.0
gca peak = 0.07177 (90)
mri peak = 0.05306 (86)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, overlap=0.860)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = 92), gca=92.2
gca peak = 0.13316 (95)
mri peak = 0.05862 (107)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels,
overlap=0.010)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak =
109),
gca=109.2
gca peak = 0.16834 (92)
mri peak = 0.06574 (111)
Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110]
rejecting
gca peak = 0.25342 (25)
mri peak = 0.12619 (24)
Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels,
overlap=0.998)
Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = 25), gca=25.0
gca peak = 0.20850 (21)
mri peak = 0.16285 (24)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels,
overlap=0.808)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak =
22),
gca=21.5
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.26363 (36)
gca peak CSF = 0.17919 (33)
gca peak Left_Accumbens_area = 0.40223 (72)
gca peak Left_VentralDC = 0.16834 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.63670 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.29122 (35)
gca peak Right_Accumbens_area = 0.25605 (83)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.81716 (36)
gca peak WM_hypointensities = 0.15216 (83)
gca peak non_WM_hypointensities = 0.09346 (54)
gca peak Optic_Chiasm = 0.34849 (76)
mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means
setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.01 x + 0.0
Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 (was 103.0)
Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6
(was
104.5)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz PREDEP40C_fsf
reading input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
mri_cc: could not read aseg volumefrom/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.
auto
_noCCseg.mgz
reading asegfrom/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.
auto
_noCCseg.mgz
ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.
auto
_noCCseg.mgz
No such file or directory
#--------------------------------------
#@# Merge ASeg Mon Feb 18 19:22:10 GMT 2013
cp aseg.auto.mgz aseg.mgz
cp: cannot stat `aseg.auto.mgz': No such file or directory
#--------------------------------------------
#@# Intensity Normalization2 Mon Feb 18 19:22:10 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: could not read aseg from file aseg.mgz
using MR volume brainmask.mgz to mask input volume...
ERROR: cannot find
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.mgz
No such file or directory
#--------------------------------------------
#@# Mask BFS Mon Feb 18 19:22:11 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
mri_mask: could not read source volume brain.mgz
ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain
.mgz
No such file or directory
#--------------------------------------------
#@# WM Segmentation Mon Feb 18 19:22:11 GMT 2013
mri_segment brain.mgz wm.seg.mgz
mri_segment: could not read source volume from brain.mgz
ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain
.mgz
No such file or directory
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz
wm.asegedit.mgz
preserving editing changes in input volume...
mri_edit_wm_with_aseg: could not read wm volume from wm.seg.mgz
reading wm segmentation from wm.seg.mgz...
ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.se
g.mg
z
No such file or directory
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
mri_pretess: could not open wm.asegedit.mgz
ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.as
eged
it.mgz
No such file or directory
#--------------------------------------------
#@# Fill Mon Feb 18 19:22:11 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume
...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...mri_fill: could not read wm.mgz
ERROR: cannot find /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.mgz
No such file or directory
#--------------------------------------------
#@# Tessellate lh Mon Feb 18 19:22:11 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
mri_pretess: could not open ../mri/filled.mgz
ERROR: cannot find ../mri/filled.mgz
No such file or directory
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
could not open ../mri/filled-pretess255.mgz
ERROR: cannot find ../mri/filled-pretess255.mgz
No such file or directory
rm -f ../mri/filled-pretess255.mgz
?
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
MRISread(../surf/lh.orig.nofix): could not open file
No such file or directory
Segmentation fault
#--------------------------------------------
#@# Smooth1 lh Mon Feb 18 19:22:12 GMT 2013
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix
../surf/lh.smoothwm.nofix
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
setting seed for random number generator to 1234
MRISread(../surf/lh.orig.nofix): could not open file
No such file or directory
mris_smooth: could not read surface file ../surf/lh.orig.nofix
No such file or directory
#--------------------------------------------
#@# Inflation1 lh Mon Feb 18 19:22:12 GMT 2013
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
MRISread(../surf/lh.smoothwm.nofix): could not open file
Not saving sulc
No such file or directory
mris_inflate: could not read surface file ../surf/lh.smoothwm.nofix
No such file or directory
#--------------------------------------------
#@# QSphere lh Mon Feb 18 19:22:12 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix
../surf/lh.qsphere.nofix
doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $
$Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
MRISread(../surf/lh.inflated.nofix): could not open file
No such file or directory
mris_sphere: could not read surface file ../surf/lh.inflated.nofix
No such file or directory
#--------------------------------------------
#@# Fix Topology lh Mon Feb 18 19:22:12 GMT 2013
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp: cannot stat `../surf/lh.orig.nofix': No such file or directory
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
cp: cannot stat `../surf/lh.inflated.nofix': No such file or directory
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234
PREDEP40C_fsf lh
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
Topology Correction Parameters
retessellation mode: genetic search
number of patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $
$Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
MRISread(/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf
/lh.qsphere.nofix): could not open file
reading inputsurface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/l
h.qsphe
re.nofix...
No such file or directory
mris_fix_topology: could not read inputsurface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/l
h.qsphe
re.nofix
No such file or directory
mris_euler_number ../surf/lh.orig
Linux ioplnx5.iop.kcl.ac.uk 2.6.32-279.19.1.el6.x86_64 #1 SMP Tue Dec 18 17:22:54 CST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013
Date: Tue, 19 Feb 2013 16:35:50 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_ca_label problem
Hi Paul
is this within recon-all? Does that file exist? Can you check its permissions to make sure it is writeable? And that you have enough
disk
space? Are any error messages printed? Bruce
On Tue, 19 Feb 2013, paul horton wrote:
Hi guys, I am wondering if you can help me. I have run command: mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
aseg.auto_noCCseg.mgz, on a 3T MPRAGE subject but it fails: i.e. it
stops
after the 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' line and does not save the
file:
aseg.auto_noCCseg.mgz. However, it does save the file: aseg.auto_noCCseg.label_intensities.txt. I have tried it several times and it stops at the same place. I have also tried recon-all, where it jumps from 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt'
to
the
command 'mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz',
where,
again,
the file: aseg.auto_noCCseg.mgz is not saved. I am using freesurfer
version
4.5.0.
So is there a way I can solve this problem.
Many Thanks Paul Ps, i have attached the output log below ################ renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifierarrayfrom/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-
03-26
.gca
... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3Dmorphwas/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-0
3-26.
gca
average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.15062 (23) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, overlap=0.484) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels,
peak
=
22), gca=22.3 gca peak = 0.14982 (20) mri peak = 0.16025 (24) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984
voxels,
overlap=0.766) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984
voxels,
peak =
20), gca=20.5 gca peak = 0.28003 (97) mri peak = 0.11295 (106) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels,
overlap=0.353)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak =
104),
gca=104.3 gca peak = 0.18160 (96) mri peak = 0.12433 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels,
overlap=0.638)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak =
101),
gca=100.8 gca peak = 0.27536 (62) mri peak = 0.08252 (69) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, overlap=0.818) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak
=
68),
gca=68.2 gca peak = 0.32745 (63) mri peak = 0.07934 (66) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak
=
65),
gca=64.6 gca peak = 0.08597 (105) mri peak = 0.06861 (109) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
voxels,
overlap=0.744) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
voxels,
peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.07113 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
voxels,
overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
voxels,
peak = 106), gca=106.0 gca peak = 0.07826 (63) mri peak = 0.02785 (72) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, overlap=0.547) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels,
peak
=
71), gca=70.9 gca peak = 0.08598 (64) mri peak = 0.02894 (68) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, overlap=0.642) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
peak =
69), gca=68.8 gca peak = 0.24164 (71) mri peak = 0.13663 (85) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels,
overlap=0.000)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak =
82),
gca=81.7 gca peak = 0.18227 (75) mri peak = 0.14739 (80) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels,
overlap=0.988)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak =
77),
gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05203 (64) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
peak =
64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.05041 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689
voxels,
overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689
voxels,
peak
= 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.09573 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
voxels,
overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
voxels,
peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.10076 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
voxels,
overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
voxels,
peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.07820 (67) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels,
overlap=1.000)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak =
66),
gca=65.6 gca peak = 0.42394 (62) mri peak = 0.10919 (71) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels,
overlap=0.434)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak =
70),
gca=69.8 gca peak = 0.10041 (96) mri peak = 0.07146 (97) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, overlap=0.910) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels,
peak
=
98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.06159 (103) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, overlap=0.376) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels,
peak
=
99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.06222 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
overlap=0.964)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak =
81),
gca=81.0 gca peak = 0.09624 (82) mri peak = 0.09383 (84) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels,
overlap=0.815)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak =
84),
gca=84.0 gca peak = 0.07543 (88) mri peak = 0.05306 (86) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels,
overlap=0.765)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak =
92),
gca=92.4 gca peak = 0.12757 (95) mri peak = 0.05862 (107) Right_VentralDC: unreasonable value (111.6/107.0), not in range [80,
110] -
rejecting gca peak = 0.17004 (92) mri peak = 0.06574 (111) Left_VentralDC: unreasonable value (105.8/111.0), not in range [80,
110]
rejecting gca peak = 0.21361 (36) mri peak = 0.12619 (24) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels,
overlap=0.000)
Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak =
25),
gca=25.2 gca peak = 0.26069 (23) mri peak = 0.16285 (24) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels,
overlap=0.640)
Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak =
21),
gca=20.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_VentralDC = 0.17004 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_VentralDC = 0.12757 (95) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5
(was
100.8) Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5
(was
104.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14515 (23) mri peak = 0.15062 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, overlap=0.897) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels,
peak
=
24), gca=23.6 gca peak = 0.19392 (21) mri peak = 0.16025 (24) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984
voxels,
overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984
voxels,
peak =
21), gca=21.0 gca peak = 0.25607 (102) mri peak = 0.11295 (106) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels,
overlap=1.000)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak =
105),
gca=104.5 gca peak = 0.17462 (103) mri peak = 0.12433 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels,
overlap=0.999)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak =
103),
gca=103.0 gca peak = 0.24759 (68) mri peak = 0.08252 (69) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak
=
68),
gca=68.0 gca peak = 0.28061 (65) mri peak = 0.07934 (66) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak
=
62),
gca=61.8 gca peak = 0.08360 (108) mri peak = 0.06861 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
voxels,
overlap=0.831) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
voxels,
peak = 108), gca=108.0 gca peak = 0.09206 (106) mri peak = 0.07113 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
voxels,
overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
voxels,
peak = 106), gca=106.0 gca peak = 0.06916 (71) mri peak = 0.02785 (72) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, overlap=0.733) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels,
peak
=
69), gca=69.2 gca peak = 0.08227 (69) mri peak = 0.02894 (68) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, overlap=0.734) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
peak =
69), gca=69.0 gca peak = 0.22329 (81) mri peak = 0.13663 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels,
overlap=1.000)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak =
81),
gca=81.0 gca peak = 0.18180 (77) mri peak = 0.14739 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels,
overlap=0.937)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak =
77),
gca=77.0 gca peak = 0.10419 (63) mri peak = 0.05203 (64) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
peak =
65), gca=64.6 gca peak = 0.12084 (64) mri peak = 0.05041 (65) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689
voxels,
overlap=0.985) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689
voxels,
peak
= 62), gca=62.4 gca peak = 0.17137 (94) mri peak = 0.09573 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
voxels,
overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
voxels,
peak = 94), gca=94.0 gca peak = 0.15715 (93) mri peak = 0.10076 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
voxels,
overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
voxels,
peak = 93), gca=93.0 gca peak = 0.32238 (65) mri peak = 0.07820 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels,
overlap=1.000)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak =
65),
gca=65.0 gca peak = 0.49832 (70) mri peak = 0.10919 (71) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels,
overlap=1.000)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak =
70),
gca=70.0 gca peak = 0.10606 (98) mri peak = 0.07146 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, overlap=0.901) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels,
peak
=
98), gca=98.0 gca peak = 0.12505 (99) mri peak = 0.06159 (103) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, overlap=0.961) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels,
peak
=
99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.06222 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
overlap=0.964)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak =
81),
gca=81.0 gca peak = 0.09838 (78) mri peak = 0.09383 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels,
overlap=0.982)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak =
78),
gca=78.0 gca peak = 0.07177 (90) mri peak = 0.05306 (86) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels,
overlap=0.860)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak =
92),
gca=92.2 gca peak = 0.13316 (95) mri peak = 0.05862 (107) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels,
overlap=0.010)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak =
109),
gca=109.2 gca peak = 0.16834 (92) mri peak = 0.06574 (111) Left_VentralDC: unreasonable value (105.8/111.0), not in range [80,
110]
rejecting gca peak = 0.25342 (25) mri peak = 0.12619 (24) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels,
overlap=0.998)
Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak =
25),
gca=25.0 gca peak = 0.20850 (21) mri peak = 0.16285 (24) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels,
overlap=0.808)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak =
22),
gca=21.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26363 (36) gca peak CSF = 0.17919 (33) gca peak Left_Accumbens_area = 0.40223 (72) gca peak Left_VentralDC = 0.16834 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.29122 (35) gca peak Right_Accumbens_area = 0.25605 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (36) gca peak WM_hypointensities = 0.15216 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6
(was
103.0) Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6
(was
104.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
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paul horton